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1 <tool id="snpEff_docker" name="SnpEff" version="3.6c (build 2014-05-20)">
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2 <description>Variant effect and annotation (Docker)</description>
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3 <requirements>
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4 <container type="docker">takakoron/snpeff_3.6c</container>
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5 </requirements>
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6 <command interpreter="perl">/usr/src/myapp/snpEffWrapper.pl eff
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7 -i $inputFormat
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8 -o $outputFormat
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9 -upDownStreamLen $udLength
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10 $canon
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11 $hgvs
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12 $lof
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13 $motif
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14 #if $statsFile:
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15 -stats $statsFile
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16 #end if
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17 $genomeVersion $input > $snpeff_output
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18 </command>
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19 <inputs>
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20 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
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21
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22 <param name="inputFormat" type="select" label="Input format">
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23 <option value="vcf" selected="true">VCF</option>
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24 <option value="txt">Tabular</option>
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25 <option value="bed">BED</option>
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26 </param>
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27
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28 <param name="outputFormat" type="select" label="Output format">
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29 <option value="vcf" selected="true">VCF</option>
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30 <option value="txt">Tabular</option>
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31 <option value="bed">BED</option>
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32 <option value="bedAnn">BED Annotations</option>
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33 <option value="gatk">VCF (GATK compatible)</option>
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34 </param>
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35
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36 <param name="genomeVersion" type="select" label="Genome" help="If your annotation of interest is not listed, contact the P-GALAXY team (pipeline_dev@ddbj.nig.ac.jp)">
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37 <options from_file="snpEff_genomes.loc">
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38 <column name="name" index="1"/>
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39 <column name="value" index="0"/>
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40 </options>
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41 </param>
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42
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43 <param name="udLength" type="select" label="Upstream / Downstream length">
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44 <option value="0">No upstream / downstream intervals (0 bases)</option>
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45 <option value="200">200 bases</option>
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46 <option value="500">500 bases</option>
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47 <option value="1000">1000 bases</option>
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48 <option value="2000">2000 bases</option>
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49 <option value="5000" selected="true">5000 bases</option>
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50 <option value="10000">10000 bases</option>
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51 <option value="20000">20000 bases</option>
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52 </param>
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53
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54 <param name="canon" type="boolean" truevalue="-canon" falsevalue="" checked="false" label="Use only cannonical transcripts"/>
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55 <param name="hgvs" type="boolean" truevalue="-hgvs" falsevalue="" checked="false" label="Annotate using HGVS nomenclature"/>
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56 <param name="lof" type="boolean" truevalue="-lof" falsevalue="" checked="false" label="Annotate Loss of function (LOF) and Nonsense mediated decay (NMD)"/>
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57 <param name="motif" type="boolean" truevalue="-motif" falsevalue="" checked="false" label="Annotate transcription factor binding site motifs (only available for latest GRCh37)"/>
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58 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
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59 </inputs>
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60 <outputs>
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61 <data format="tabular" name="snpeff_output" >
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62 <change_format>
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63 <when input="outputFormat" value="txt" format="tabular" />
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64 <when input="outputFormat" value="vcf" format="vcf" />
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65 <when input="outputFormat" value="bed" format="bed" />
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66 <when input="outputFormat" value="bedAnn" format="bed" />
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67 </change_format>
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68 </data>
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69
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70 <data format="html" name="statsFile">
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71 <filter>generate_stats == True</filter>
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72 </data>
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73 </outputs>
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74 <stdio>
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75 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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76 <exit_code range="1:" level="fatal" description="Error" />
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77 </stdio>
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78 <tests>
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79 <test>
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80 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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81 <param name="inputFormat" value="vcf"/>
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82 <param name="outputFormat" value="vcf"/>
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83 <param name="genomeVersion" value="testCase"/>
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84 <param name="udLength" value="0"/>
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85 <output name="snpeff_output">
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86 <assert_contents>
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87 <!-- Check that an effect was added -->
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88 <has_text text="EFF=NON_SYNONYMOUS_CODING" />
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89 </assert_contents>
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90 </output>
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91 <output name="statsFile">
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92 <assert_contents>
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93 <!-- Check for a HTML header indicating that this was successful -->
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94 <has_text text="SnpEff: Variant analysis" />
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95 </assert_contents>
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96 </output>
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97 </test>
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98 </tests>
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99 <help>
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100
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101 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
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102
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103 For details about this tool, please go to http://snpEff.sourceforge.net
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104
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105 </help>
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106 </tool>
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107
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